Survival Curves
Plasma_peptide26gp120_antibody_response__WkPost vs Plasma_AvidityScore_cV2gp120__WkPost
14 up and 2 down pairs with p < 0.05
17 up and 0 down pairs with p < 0.05
Plasma_ADCC_Killing__WkPost vs Plasma_gp120_antibody_titers__WkPost
Plasma_ADCP_SIVgp120dV1__Change vs Plasma_ADNP_SIVgp120dV1__Change
Plasma_Trogocytosis_dV1gp120__Change vs Plasma_ADNP_SIVgp120dV1__Change
Plasma_AvidityScore_dV1M766gp120__WkPost vs Plasma_ADNP_SIVgp120dV1__Change
PBMCs_PctCD14_efferocytes__WkPost vs RectMucosa_CD73posCD163posMacrophages__Change
24 up and 3 down pairs with p < 0.05
16 up and 1 down pairs with p < 0.05
FACS scheme
RectMucosa_CD73posCD163posMacrophages__Change vs Vaginal_secretions_dV1gp120_antibody_titers__WkPost
RectMucosa_CD73posCD163posMacrophages__Change vs RectMucosa_CD73posDC10__Change
RectMucosa_DC10__WkPost vs RectMucosa_NKp44__WkPost
RectMucosa_CD163posMacrophages__Change vs RectMucosa_NKp44__Change
RectMucosa_CD163posMacrophages__Change vs RectMucosa_NKp44negNKG2Aneg_PMA_IFNg__Change
RectMucosa_CD73posCD163posMacrophages__WkPost vs RectMucosa_NKp44negNKG2Aneg_PMA_IFNg__WkPost
Plasma_V2specific_ADCC_Killing__WkPost vs RectMucosa_NKp44__Change
SuppFig4j
ellipse = 95 % normal probability
top 5 loadings per PC displayed
17 ALUM + 12 ALFQA animals in PCA
ellipse = 95 % normal probability
top 5 loadings per PC displayed
12 ALUM + 12 ALFQA animals in PCA
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
baseline same assays, without Baseline
ellipse = 95 % normal probability
top 5 loadings per PC displayed
12 ALUM + 12 ALFQA animals in PCA
x-axis: log10(abs(MW estimate x100)) x sign of MW estimate
MW estimate = median of outer differences
outer differences = difference between all pairs of values in group1 - group2, e.g. for A = a1, a2 and B = b1, b2; then the outer differences would be: a1-b1, a2-b1, a1-b2, a2-b2. And the MW estimate is the median of these deltas. For MW estimate > 0, ALFQA > ALUM; and for MW estmate < 0, ALFQA < ALUM
x100 = to shift all estimates > 1 (or < -1) so that the log10 does not transform values -1 < x < 1; thus for a MW estimate of 0.01 (the smallest magnitude estimate) –> log10(0.01 x100) = 0
Baseline diff only
2 up and 0 down pairs with p < 0.001
6 up and 0 down pairs with p < 0.001
8 up and 0 down pairs with p < 0.001
8 up and 0 down pairs with p < 0.001
1 up and 0 down pairs with p < 0.001
10 up and 0 down pairs with p < 0.001
For IPA (see methods)
For IPA (see methods)
For IPA (see methods)
For IPA (see methods)
RectMucosa_DC10__Change vs LTA__wk13
Summary of variables different ALFQA vs Alum, associations with TOA
RectMucosa_DC10__Change vs MMP12__wk12_24h
RectMucosa_DC10__Change vs CCL13__wk12_24h
RectMucosa_DC10__Change vs VEGFA__wk12_24h
CXCL8__wk13 vs EGF__wk13
Mann-Whitney/Wilcoxon test between groups at each timepoint
Spearman correlation between TOA and assays, or among assays
Excel spreadsheet of stats## R version 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS 15.5
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
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##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
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## [4] dendextend_1.17.1 dendsort_0.3.4 strex_2.0.1
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